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Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.

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r-phosr 1.20.0
Propagated dependencies: r-tidyr@1.3.1 r-summarizedexperiment@1.38.1 r-stringi@1.8.7 r-s4vectors@0.46.0 r-ruv@0.9.7.1 r-rlang@1.1.6 r-reshape2@1.4.4 r-rcolorbrewer@1.1-3 r-preprocesscore@1.70.0 r-pheatmap@1.0.12 r-pcamethods@2.0.0 r-network@1.19.0 r-limma@3.64.1 r-igraph@2.1.4 r-ggtext@0.1.2 r-ggpubr@0.6.0 r-ggplot2@3.5.2 r-ggdendro@0.2.0 r-ggally@2.2.1 r-e1071@1.7-16 r-dplyr@1.1.4 r-dendextend@1.19.0 r-circlize@0.4.16 r-biocgenerics@0.54.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PhosR
Licenses: FSDG-compatible
Synopsis: set of methods and tools for comprehensive analysis of phosphoproteomics data
Description:

PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.

r-ppinfer 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PPInfer
Licenses: Artistic License 2.0
Synopsis: Inferring functionally related proteins using protein interaction networks
Description:

Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.

r-primeviewcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/primeviewcdf
Licenses: LGPL 2.0+
Synopsis: primeviewcdf
Description:

This package provides a package containing an environment representing the PrimeView.cdf file.

r-pd-rg-u34b 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.rg.u34b
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name RG_U34B
Description:

Platform Design Info for The Manufacturer's Name RG_U34B.

r-pd-mirna-1-0 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mirna.1.0
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name miRNA-1_0
Description:

Platform Design Info for The Manufacturer's Name miRNA-1_0.

r-pd-mirna-2-0 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mirna.2.0
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix miRNA-2_0
Description:

Platform Design Info for Affymetrix miRNA-2_0.

r-pd-hg18-60mer-expr 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.hg18.60mer.expr
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for NimbleGen hg18_60mer_expr
Description:

Platform Design Info for NimbleGen hg18_60mer_expr.

r-pedbarrayv9-db 3.2.3
Propagated dependencies: r-org-hs-eg-db@3.21.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pedbarrayv9.db
Licenses: Artistic License 2.0
Synopsis: FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9)
Description:

FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.

r-pepxmltab 1.44.0
Propagated dependencies: r-xml@3.99-0.18
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pepXMLTab
Licenses: Artistic License 2.0
Synopsis: Parsing pepXML files and filter based on peptide FDR
Description:

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

r-pd-clariom-s-human 3.14.1
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.clariom.s.human
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix Clariom_S_Human
Description:

Platform Design Info for Affymetrix Clariom_S_Human.

r-pd-ragene-1-0-st-v1 3.14.1
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.ragene.1.0.st.v1
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix RaGene-1_0-st-v1
Description:

Platform Design Info for Affymetrix RaGene-1_0-st-v1.

r-pd-hugene-1-1-st-v1 3.14.1
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.hugene.1.1.st.v1
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix HuGene-1_1-st-v1
Description:

Platform Design Info for Affymetrix HuGene-1_1-st-v1.

r-pengls 1.16.0
Propagated dependencies: r-nlme@3.1-168 r-glmnet@4.1-8 r-biocparallel@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/sthawinke/pengls
Licenses: GPL 2
Synopsis: Fit Penalised Generalised Least Squares models
Description:

Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.

r-plier 1.80.0
Propagated dependencies: r-biobase@2.68.0 r-affy@1.86.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/plier
Licenses: GPL 2+
Synopsis: Implements the Affymetrix PLIER algorithm
Description:

The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.

r-paeg1acdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/paeg1acdf
Licenses: LGPL 2.0+
Synopsis: paeg1acdf
Description:

This package provides a package containing an environment representing the Pae_G1a.CDF file.

r-prostatecancervarambally 1.38.0
Propagated dependencies: r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/prostateCancerVarambally
Licenses: Artistic License 2.0
Synopsis: Prostate Cancer Data
Description:

This package provides a Bioconductor data package for the Varambally dataset.

r-pd-medicago 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.medicago
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name Medicago
Description:

Platform Design Info for The Manufacturer's Name Medicago.

r-pathwaypca 1.26.0
Propagated dependencies: r-survival@3.8-3 r-lars@1.3
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: <https://gabrielodom.github.io/pathwayPCA/>
Licenses: GPL 3
Synopsis: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Description:

pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>; Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.

r-pvca 1.50.0
Propagated dependencies: r-vsn@3.76.0 r-matrix@1.7-3 r-lme4@1.1-37 r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pvca
Licenses: LGPL 2.0+
Synopsis: Principal Variance Component Analysis (PVCA)
Description:

This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.

r-phipdata 1.18.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-s4vectors@0.46.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-edger@4.6.2 r-cli@3.6.5 r-biocgenerics@0.54.0 r-biocfilecache@2.16.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PhIPData
Licenses: Expat
Synopsis: Container for PhIP-Seq Experiments
Description:

PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

r-pd-fingene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.fingene.1.0.st
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix FinGene-1_0-st
Description:

Platform Design Info for Affymetrix FinGene-1_0-st.

r-pd-wheat 3.12.0
Propagated dependencies: r-s4vectors@0.46.0 r-rsqlite@2.3.11 r-oligoclasses@1.70.0 r-oligo@1.72.0 r-iranges@2.42.0 r-dbi@1.2.3 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.wheat
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for The Manufacturer's Name wheat
Description:

Platform Design Info for The Manufacturer's Name wheat.

r-peakcombiner 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/novartis/peakCombiner/
Licenses: Expat
Synopsis: The R package to curate and merge enriched genomic regions into consensus peak sets
Description:

peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

r-prostatecancergrasso 1.38.0
Propagated dependencies: r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/prostateCancerGrasso
Licenses: Artistic License 2.0
Synopsis: Prostate Cancer Data
Description:

This package provides a Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.

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Total results: 45109